Most cited papers in Genomics and Phylogenetic Studies
What are the most cited papers in Genomics and Phylogenetic Studies?
The most cited paper in Genomics and Phylogenetic Studies is "Cleavage of Structural Proteins during the Assembly of the Head of Bacteriophage T4" (Ulrich K. Laemmli, 1970), with 252,153 citations. Next come "Basic local alignment search tool" (95,803) and "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs" (75,032).
Showing 50 of 100 papers. Every paper with more than 11,822 citations is listed.
| # | Paper | ||
|---|---|---|---|
| 1 | Cleavage of Structural Proteins during the Assembly of the Head of Bacteriophage T4 Ulrich K. Laemmli · Nature | Aug 1970 | 252,153 |
| 2 | Basic local alignment search tool Stephen F. Altschul, Warren R. Gish, Webb Miller et al. · Journal of Molecular Biology | Oct 1990 | 95,803 |
| 3 | Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Stephen F. Altschul · Nucleic Acids Research | Sep 1997 | 75,032 |
| 4 | Fiji: an open-source platform for biological-image analysis Johannes Schindelin, Ignacio Arganda‐Carreras, Erwin Frise et al. · Nature Methods | 28 Jun 2012 | 73,171 |
| 5 | Trimmomatic: a flexible trimmer for Illumina sequence data Anthony Bolger, Marc Lohse, Björn Usadel · Bioinformatics | Apr 2014 | 71,819 |
| 6 | The Sequence Alignment/Map format and SAMtools Heng Li, Bob Handsaker, Alec Wysoker et al. · Bioinformatics | 8 Jun 2009 | 69,061 |
| 7 | CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Julie Thompson, Desmond G. Higgins, Toby J. Gibson · Nucleic Acids Research | 1994 | 65,356 |
| 8 | Fast and accurate short read alignment with Burrows–Wheeler transform Heng Li, Richard M. Durbin · Bioinformatics | 18 May 2009 | 63,989 |
| 9 | Fast gapped-read alignment with Bowtie 2 Ben Langmead, Steven L. Salzberg · Nature Methods | 4 Mar 2012 | 62,825 |
| 10 | The neighbor-joining method: a new method for reconstructing phylogenetic trees. Naruya Saitou, M Nei · Molecular Biology and Evolution | Jul 1987 | 60,643 |
| 11 | STAR: ultrafast universal RNA-seq aligner Alexander Yu. Dobin, Carrie Davis, Felix Schlesinger et al. · Bioinformatics | 25 Oct 2012 | 58,026 |
| 12 | MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability Kazutaka Katoh, Daron M. Standley · Molecular Biology and Evolution | 16 Jan 2013 | 50,020 |
| 13 | MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0 Koichiro Tamura, Glen Stecher, Daniel S. Peterson et al. · Molecular Biology and Evolution | 16 Oct 2013 | 48,154 |
| 14 | MUSCLE: multiple sequence alignment with high accuracy and high throughput R. C. Edgar · Nucleic Acids Research | 8 Mar 2004 | 47,285 |
| 15 | MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets Sudhir Kumar, Glen Stecher, Koichiro Tamura · Molecular Biology and Evolution | 22 Mar 2016 | 46,273 |
| 16 | MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods Koichiro Tamura, Daniel Gunnar Peterson, Nora Peterson et al. · Molecular Biology and Evolution | 4 May 2011 | 40,453 |
| 17 | MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms Sudhir Kumar, Glen Stecher, Michael M. Li et al. · Molecular Biology and Evolution | May 2018 | 39,563 |
| 18 | The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Julie Thompson · Nucleic Acids Research | 15 Dec 1997 | 39,325 |
| 19 | Cutadapt removes adapter sequences from high-throughput sequencing reads Marcel Martin · EMBnet journal | 2 May 2011 | 37,060 |
| 20 | QIIME allows analysis of high-throughput community sequencing data J. Gregory Caporaso et al. · Nature Methods | 11 Apr 2010 | 36,341 |
| 21 | The SILVA ribosomal RNA gene database project: improved data processing and web-based tools Christian Quast, Elmar Pruesse, Pelin Yilmaz et al. · Nucleic Acids Research | 27 Nov 2012 | 35,094 |
| 22 | RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies Alexandros Stamatakis · Bioinformatics | 21 Jan 2014 | 34,939 |
| 23 | KEGG: Kyoto Encyclopedia of Genes and Genomes Hiroyuki Ogata, Susumu Goto, Kazushige Sato et al. · Nucleic Acids Research | 1999 | 32,529 |
| 24 | BEDTools: a flexible suite of utilities for comparing genomic features Aaron R. Quinlan, Ira M. Hall · Bioinformatics | 28 Jan 2010 | 31,302 |
| 25 | The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data Aaron McKenna, Matthew G. Hanna, Eric Banks et al. · Genome Research | 19 Jul 2010 | 30,696 |
| 26 | featureCounts: an efficient general purpose program for assigning sequence reads to genomic features Yang Liao, Gordon K. Smyth, Wei Shi · Bioinformatics | 13 Nov 2013 | 30,361 |
| 27 | A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences Motoo Kimura · Journal of Molecular Evolution | Jun 1980 | 30,129 |
| 28 | MrBayes 3: Bayesian phylogenetic inference under mixed models Fredrik Ronquist, John P. Huelsenbeck · Bioinformatics | 11 Aug 2003 | 29,587 |
| 29 | Clustal W and Clustal X version 2.0 Mark Larkin, Gordon Blackshields, Nigel P. Brown et al. · Bioinformatics | 10 Sep 2007 | 29,302 |
| 30 | MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0 Koichiro Tamura, Joel T. Dudley, M Nei et al. · Molecular Biology and Evolution | 18 Apr 2007 | 28,894 |
| 31 | MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space Fredrik Ronquist, Maxim Teslenko, Paul van der Mark et al. · Systematic Biology | 22 Feb 2012 | 28,705 |
| 32 | IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies Lam-Tung Nguyen, Heiko A. Schmidt, Arndt von Haeseler et al. · Molecular Biology and Evolution | 3 Nov 2014 | 28,418 |
| 33 | SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing Anton Bankevich, Sergey Nurk, Dmitry Antipov et al. · Journal of Computational Biology | 16 Apr 2012 | 27,967 |
| 34 | HISAT: a fast spliced aligner with low memory requirements Daehwan Kim, Ben Langmead, Steven L. Salzberg · Nature Methods | 9 Mar 2015 | 26,880 |
| 35 | Initial sequencing and analysis of the human genome Eric S. Lander et al. · Nature | Feb 2001 | 24,745 |
| 36 | BLAST+: architecture and applications Christiam Camacho, George Coulouris, Vahram Avagyan et al. · BMC Bioinformatics | Dec 2009 | 24,075 |
| 37 | RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome Bo Li, Colin N. Dewey · BMC Bioinformatics | 4 Aug 2011 | 24,027 |
| 38 | MEGA11: Molecular Evolutionary Genetics Analysis Version 11 Koichiro Tamura, Glen Stecher, Sudhir Kumar · Molecular Biology and Evolution | 22 Apr 2021 | 23,365 |
| 39 | Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Ben Langmead, Cole Trapnell, Mihai Pop et al. · Genome biology | 4 Mar 2009 | 23,344 |
| 40 | phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data Paul J. McMurdie, Susan Holmes · PLoS ONE | 22 Apr 2013 | 23,323 |
| 41 | HTSeq—a Python framework to work with high-throughput sequencing data Simon Anders, Paul Theodor Pyl, Wolfgang K. Huber · Bioinformatics | 25 Sep 2014 | 23,242 |
| 42 | Full-length transcriptome assembly from RNA-Seq data without a reference genome Manfred G. Grabherr et al. · Nature Biotechnology | 15 May 2011 | 23,028 |
| 43 | MRBAYES: Bayesian inference of phylogenetic trees John P. Huelsenbeck, Fredrik Ronquist · Bioinformatics | Aug 2001 | 22,339 |
| 44 | Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities Patrick D. Schloss, Sarah L. Westcott, Thomas Ryabin et al. · Applied and Environmental Microbiology | 3 Oct 2009 | 22,073 |
| 45 | Search and clustering orders of magnitude faster than BLAST R. C. Edgar · Bioinformatics | 12 Aug 2010 | 22,013 |
| 46 | Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data Matthew D. Kearse, Richard Moir, Amy Swango Wilson et al. · Bioinformatics | 27 Apr 2012 | 21,229 |
| 47 | Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy Qiong Wang, George M Garrity, James M. Tiedje et al. · Applied and Environmental Microbiology | 22 Jun 2007 | 20,801 |
| 48 | A global reference for human genetic variation Corresponding authors et al. · Nature | 29 Sep 2015 | 20,444 |
| 49 | Prokka: rapid prokaryotic genome annotation Torsten Seemann · Bioinformatics | 18 Mar 2014 | 20,396 |
| 50 | MODELTEST: testing the model of DNA substitution. David Posada, Keith A. Crandall · Bioinformatics | 1998 | 20,136 |
Citations are OpenAlex's own counts, from its 2026-09-23 snapshot, so the ranking can differ from Google Scholar or Web of Science. A paper is listed for a field when OpenAlex files it under one of the field's topics; retracted papers and papers whose citation count cannot be traced to citing works are left out, and a preprint and the article it became are shown once. Release dates are OpenAlex's: where a source gave only a month or a year, that is what is shown. How the lists are chosen.